Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG.

Eukaryotes have one replicative helicase known as CMG, which centrally organizes and drives the replisome, and leads the way at the front of replication forks. Obtaining a deep mechanistic understanding of the dynamics of CMG is critical to elucidating how cells achieve the enormous task of efficiently and accurately replicating their entire genome once per cell cycle. Single-molecule techniques are uniquely suited to quantify the dynamics of CMG due to their unparalleled temporal and spatial resolution. Nevertheless, single-molecule studies of CMG motion have thus far relied on pre-formed CMG purified from cells as a complex, which precludes the study of the steps leading up to its activation. Here, we describe a hybrid ensemble and single-molecule assay that allowed imaging at the single-molecule level of the motion of fluorescently labeled CMG after fully reconstituting its assembly and activation from 36 different purified S. cerevisiae polypeptides. This assay relies on the double functionalization of the ends of a linear DNA substrate with two orthogonal attachment moieties, and can be adapted to study similarly complex DNA-processing mechanisms at the single-molecule level.

A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy.

Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force-fluorescence spectroscopy apparatus broadly used to investigate various biological processes, in particular, protein:DNA interactions. Such experiments typically involve imaging of fluorescently labeled proteins bound to DNA and force spectroscopy measurements of trapped individual DNA molecules. Here, we present a versatile state-of-the-art toolbox including the preparation of protein:DNA complex samples, design of a microfluidic flow cell incorporated with OT, automation of OT-confocal scanning measurements, and the development and implementation of a streamlined data analysis package for force and fluorescence spectroscopy data processing. Its components can be adapted to any commercialized or home-built dual-beam OT setup equipped with a confocal scanning microscope, which will facilitate single-molecule force-fluorescence spectroscopy studies on a large variety of biological systems.

Automated cell counting for Trypan blue-stained cell cultures using machine learning.

Cell counting is a vital practice in the maintenance and manipulation of cell cultures. It is a crucial aspect of assessing cell viability and determining proliferation rates, which are integral to maintaining the health and functionality of a culture. Additionally, it is critical for establishing the time of infection in bioreactors and monitoring cell culture response to targeted infection over time. However, when cell counting is performed manually, the time involved can become substantial, particularly when multiple cultures need to be handled in parallel. Automated cell counters, which enable significant time reduction, are commercially available but remain relatively expensive. Here, we present a machine learning (ML) model based on YOLOv4 that is able to perform cell counts with a high accuracy (>95%) for Trypan blue-stained insect cells. Images of two distinctly different cell lines, Trichoplusia ni (High FiveTM; Hi5 cells) and Spodoptera frugiperda (Sf9), were used for training, validation, and testing of the model. The ML model yielded F1 scores of 0.97 and 0.96 for alive and dead cells, respectively, which represents a substantially improved performance over that of other cell counters. Furthermore, the ML model is versatile, as an F1 score of 0.96 was also obtained on images of Trypan blue-stained human embryonic kidney (HEK) cells that the model had not been trained on. Our implementation of the ML model comes with a straightforward user interface and can image in batches, which makes it highly suitable for the evaluation of multiple parallel cultures (e.g. in Design of Experiments). Overall, this approach for accurate classification of cells provides a fast, bias-free alternative to manual counting.

A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint.

Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin recognition sequences. However, less is known about the dynamics of ORC proteins in the presence of nucleosomes and attendant consequences for MCM loading. To address this, we harnessed an in vitro single-molecule approach to interrogate a chromatinized origin of replication. We find that ORC binds the origin of replication with similar efficiency independently of whether the origin is chromatinized, despite ORC mobility being reduced by the presence of nucleosomes. Recruitment of MCM also proceeds efficiently on a chromatinized origin, but subsequent movement of MCM away from the origin is severely constrained. These findings suggest that chromatinized origins in yeast are essential for the local retention of MCM, which may facilitate subsequent assembly of the replisome.

Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation.

The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that has been reconstituted from purified proteins in ensemble biochemical studies. Conversely, single-molecule studies of CMG motion have thus far relied on pre-formed CMG assembled through an unknown mechanism upon overexpression of individual constituents. Here, we report the activation of CMG fully reconstituted from purified yeast proteins and the quantification of its motion at the single-molecule level. We observe that CMG can move on DNA in two ways: by unidirectional translocation and by diffusion. We demonstrate that CMG preferentially exhibits unidirectional translocation in the presence of ATP, whereas it preferentially exhibits diffusive motion in the absence of ATP. We also demonstrate that nucleotide binding halts diffusive CMG independently of DNA melting. Taken together, our findings support a mechanism by which nucleotide binding allows newly assembled CMG to engage with the DNA within its central channel, halting its diffusion and facilitating the initial DNA melting required to initiate DNA replication.

DNA replication origins retain mobile licensing proteins.

DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which, with Cdc6 and Cdt1, recruits and loads the Mcm2-7 (MCM) helicase as an inactive double hexamer during G1 phase. The replisome assembles at the activated helicase in S phase. Although the outline of replisome assembly is understood, little is known about the dynamics of individual proteins on DNA and how these contribute to proper complex formation. Here we show, using single-molecule optical trapping and confocal microscopy, that yeast ORC is a mobile protein that diffuses rapidly along DNA. Origin recognition halts this search process. Recruitment of MCM molecules in an ORC- and Cdc6-dependent fashion results in slow-moving ORC-MCM intermediates and MCMs that rapidly scan the DNA. Following ATP hydrolysis, salt-stable loading of MCM single and double hexamers was seen, both of which exhibit salt-dependent mobility. Our results demonstrate that effective helicase loading relies on an interplay between protein diffusion and origin recognition, and suggest that MCM is stably loaded onto DNA in multiple forms.

How Substitutional Point Defects in Two-Dimensional WS2 Induce Charge Localization, Spin-Orbit Splitting, and Strain.

Control of impurity concentrations in semiconducting materials is essential to device technology. Because of their intrinsic confinement, the properties of two-dimensional semiconductors such as transition metal dichalcogenides (TMDs) are more sensitive to defects than traditional bulk materials. The technological adoption of TMDs is dependent on the mitigation of deleterious defects and guided incorporation of functional foreign atoms. The first step toward impurity control is the identification of defects and assessment of their electronic properties. Here, we present a comprehensive study of point defects in monolayer tungsten disulfide (WS2) grown by chemical vapor deposition using scanning tunneling microscopy/spectroscopy, CO-tip noncontact atomic force microscopy, Kelvin probe force spectroscopy, density functional theory, and tight-binding calculations. We observe four different substitutional defects: chromium (CrW) and molybdenum (MoW) at a tungsten site, oxygen at sulfur sites in both top and bottom layers (OS top/bottom), and two negatively charged defects (CD type I and CD type II). Their electronic fingerprints unambiguously corroborate the defect assignment and reveal the presence or absence of in-gap defect states. CrW forms three deep unoccupied defect states, two of which arise from spin-orbit splitting. The formation of such localized trap states for CrW differs from the MoW case and can be explained by their different d shell energetics and local strain, which we directly measured. Utilizing a tight-binding model the electronic spectra of the isolectronic substitutions OS and CrW are mimicked in the limit of a zero hopping term and infinite on-site energy at a S and W site, respectively. The abundant CDs are negatively charged, which leads to a significant band bending around the defect and a local increase of the contact potential difference. In addition, CD-rich domains larger than 100 nm are observed, causing a work function increase of 1.1 V. While most defects are electronically isolated, we also observed hybrid states formed between CrW dimers. The important role of charge localization, spin-orbit coupling, and strain for the formation of deep defect states observed at substitutional defects in WS2 as reported here will guide future efforts of targeted defect engineering and doping of TMDs.

Anisotropic ultraviolet-plasmon dispersion in black phosphorus.

By means of momentum-resolved electron energy loss spectroscopy (EELS) coupled with scanning transmission electron microscopy, we have studied the dispersion relation of interband plasmonic modes in the ultraviolet in black phosphorus. We find that the dispersion of the interband plasmons is anisotropic. Experimental results are reproduced by density functional theory, by taking into account both the anisotropy of the single-particle response function, arising from the anisotropic band structure, and the damping. Moreover, our theoretical model also indicates the presence of low-energy excitations in the near-infrared that are selectively active in the armchair direction, whose existence has been experimentally validated by high-resolution EELS (HREELS) in reflection mode.